Dear experts,
I recently installed dmriprep using following set of commands:
git clone https://github.com/nipy/dmriprep
cd dmriprep
make docker
After installing it I am ran the following command to run dmriprep:
docker run -ti -v $input_bids_dir:/inputs -v $output_derivatives_dir:/outputs dmriprep:prod dmriprep /inputs /outputs
When I run the above I get following error:
If you are considering commercial use of this container, please consult the relevant license:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
/opt/miniconda-latest/envs/dmriprep/lib/python3.6/site-packages/bids/layout/models.py:152: FutureWarning: The ‘extension’ entity currently excludes the leading dot (’.’). As of version 0.14.0, it will include the leading dot. To suppress this warning and include the leading dot, usebids.config.set_option('extension_initial_dot', True).
FutureWarning)
Traceback (most recent call last):
File “/opt/miniconda-latest/envs/dmriprep/bin/dmriprep”, line 33, in
sys.exit(load_entry_point(‘dmriprep==0.1.0’, ‘console_scripts’, ‘dmriprep’)())
File “/opt/miniconda-latest/envs/dmriprep/lib/python3.6/site-packages/click/core.py”, line 829, in call
return self.main(*args, **kwargs)
File “/opt/miniconda-latest/envs/dmriprep/lib/python3.6/site-packages/click/core.py”, line 782, in main
rv = self.invoke(ctx)
File “/opt/miniconda-latest/envs/dmriprep/lib/python3.6/site-packages/click/core.py”, line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “/opt/miniconda-latest/envs/dmriprep/lib/python3.6/site-packages/click/core.py”, line 610, in invoke
return callback(*args, **kwargs)
File “/opt/miniconda-latest/envs/dmriprep/lib/python3.6/site-packages/dmriprep-0.1.0-py3.6.egg/dmriprep/cli.py”, line 69, in main
inputs = io.get_bids_files(participant_label, bids_dir)
File “/opt/miniconda-latest/envs/dmriprep/lib/python3.6/site-packages/dmriprep-0.1.0-py3.6.egg/dmriprep/io.py”, line 82, in get_bids_files
return [get_bids_subject_input_files(sub, bids_input_directory) for sub in subjects]
File “/opt/miniconda-latest/envs/dmriprep/lib/python3.6/site-packages/dmriprep-0.1.0-py3.6.egg/dmriprep/io.py”, line 82, in
return [get_bids_subject_input_files(sub, bids_input_directory) for sub in subjects]
File “/opt/miniconda-latest/envs/dmriprep/lib/python3.6/site-packages/dmriprep-0.1.0-py3.6.egg/dmriprep/io.py”, line 28, in get_bids_subject_input_files
extensions=[’.nii’, ‘.nii.gz’])
File “/opt/miniconda-latest/envs/dmriprep/lib/python3.6/site-packages/bids/layout/layout.py”, line 630, in get
raise ValueError(msg + "If you’re sure you want to impose "
ValueError: ‘extensions’ is not a recognized entity. Did you mean [‘extension’]? If you’re sure you want to impose this constraint, set invalid_filters=‘allow’.
May you please suggest how to resolve this?
Thank you,
Sneha